SARS-CoV-2 NSP14 Inhibitor Confers Potent Antiviral Efficacy and Reverses NSP14-triggered Host Cell Modulation

The emergence of SARS-CoV-2 variants and drug-resistant mutants necessitates additional antivirals. SARS-CoV-2 NSP14 N7-guanosine methyltransferase is responsible for viral RNA capping, facilitating replication and evading immune detection. NSP14 has emerged as a promising drug target, but the role of NSP14 in host-virus crosstalk and the cellular effects of NSP14 inhibition are poorly understood. Here, we performed structure-based virtual screen to identify non-nucleoside inhibitors targeting NSP14 SAM-binding pocket. Hit to Lead optimization resulted in the development of C10 that potently inhibited SARS-CoV-2 and variants with the EC50 values from 64.03 to 301.9 nM, comparable to FDA-approved drug remdesivir in our cell-based model. C10 is a selective inhibitor of β-coronavirus NSP14 and directly suppresses SARS-CoV-2 replication, as demonstrated by a SARS-CoV-2 replicon system. C10 specifically reversed NSP14-mediated host transcriptome alterations and, phenotypically, restored host cell cycle progression disrupted by NSP14. The antiviral efficacy of C10 was further validated in a transgenic mouse model of SARS-CoV-2 infection. Our findings indicate C10 holds promise for developing effective treatments against SARS-CoV-2 and emerging variants, as well as uncover a novel pathogenic role of NSP14 beyond its function in viral RNA capping, which may be also adaptable to other viral capping methyltransferase. RNA-sequencing (RNA-seq) of cells expressing nsp14 treated by C7 or C10 to reveal its molecular effects on host cells.